The $40 is refunded when your reservation is shipped or if you cancel your reservation prior to it shipping, so it's not an additional cost.
I'd still go with the Nexus if I were you, the screen is just so much better than anything else out there.

i think i'll just wait, i'm in a small town so i might luck out and get to pick one up, it says that even stores that have none reserved will be getting stock and if you find one at a store and pick it up you can then cancel your reservation. i'd rather know what the cost of the upgrade is before i commit so i'm going into the store tomorrow and see what they say.

The upgrade price is rumoured to be $160 on the Nexus, but not confirmed.
Plus you have to take into account if you're doing an early upgrade which will have additional fees.
If you don't have any early upgrade fees on the S2LTE, you won't have any on the Nexus.